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Old 11-21-2014, 08:57 AM   #14
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You have VERY few reads. You might want to view the alignments in IGV or a similar program and see if you actually have any alignments to genes or not. Also, you can use the -o option to see how individual alignments are being treated. This is quite useful to debug things.
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